NSF ADBC Digitization TCN-TTD Plants, Herbivores, and
Parasitoids A Model System for the study of Tri-Trophic
Associations Ten months later presentation by Randall Schuh,
American Museum of Natural History Rob Naczi, New York Botanical
Garden Christiane Weirauch, University of California Riverside
Katja Seltmann, American Museum of Natural History,
http://tcn.amnh.org Slide 2 The Tri-Trophic Approach Capturing Data
for the Nearctic Biota 85% of 11,000 Hemiptera from the Nearctic
are herbivorous with high host specificity Bias in plant groups
attacked, e.g.,, Pinaceae, Poaceae, Asteraceae, Chenopodiaceae,
Rosaceae Some serious agricultural pests (armored scales, mealy
bugs, potato leafhoppers, Lygus bugs) Vectors of viral and
bacterial diseases (green peach aphid is a vector of over 100 plant
viruses) Parasitic Hymenoptera are beneficial as biological control
agents Slide 3 MICH MO NYBG EMC WIS MIN KANU ISC COLO MAINE MU TEX
ILL ILLS Botanical Institutions Slide 4 MICH MO NYBG EMC WIS MIN
KANU ISC COLO MAINE MU TEX ILL ILLS SEINET CCH CPNH Botanical
Institutions Botanical Data Providers Slide 5 MICH MO NYBG EMC WIS
MIN KANU ISC COLO MAINE MU TEX ILL ILLS SEINET CCH CPNH AMNH CDFA
UCRC CAS BPBM MEM CMNH INHS CUIC CSUC TAMU OSAC NCSU SEMC UDCC EMEC
UMEC UKIC Botanical Institutions Botanical Data Providers
Entomological Collections Slide 6 Project management Steering
Committee of 10 PIs + Project Manager Decision-making on overall
project goals, directions, and progress Full-time Project Manager
at AMNH (Katja Seltmann) Day-to-day project management, technical
capability, data analysis, training of entomology partners, vetting
and upload of authority files, centralized georeferencing Full-time
Project Coordinator at NYBG (Kim Watson) Training of botany
partners, barcoding of NYBG specimens, and label-data capture for
all partner institutions Slide 7 Entomological Databasing Slide 8
Streamlined Interface for Rapid Data Entry Taxon names Locality
data Collection Events Specimen Data Host names Slide 9 Database
Attributes Web enabled Open-source software Centralized data
storage, backup, and management Database Benefits Single-product
management Simplified user training Centralized authority-file
management Centralized georeferencing Data aggregation shifted to
HUB and DiscoverLife.org Slide 10 Authority Files Botanical
Tropicos database used across entire project Entomological
Published catalogs and unpublished lists from specialists
Objectives Present uniform up-to-date taxonomy Reduce decision
making by data-entry personnel Limit entry of new names by
data-entry personnel Slide 11 Data Aggregation and Dissemination
------------------------ leveraging DiscoverLife.org Slide 12 Slide
13 Slide 14 Approaches to Outreach AMNH Short Course in Collection
Databasing Fundamentals Train graduate-students through
participant-support funding Involve students from multiple graduate
programs Provide fundamentals, including database options, data
structures, unique specimen identification, specimen handling,
georeferencing, research tools, data dissemination Undergraduate
Research Projects REU projects joining project data to student
research involvement Community Outreach
http://research.amnh.org/pbi/heteropteraspeciespage/ Slide 15 Rob
Naczi New York Botanical Garden Slide 16 Botanical Specimen Imaging
Slide 17 Insect Specimen Imaging Image representative specimens for
each species Use existing imaging stations at partner institutions
About 30% of Hemiptera are already imaged Expect to produce about
20,000 new images Slide 18 Use of OCR for Populating Botanical
Records Workflow jpgs of specimen sheets batch-cropped to labels
labels saved as new set of jpgs, then exported to ABBYY Fine Reader
11 Corporate Edition overnight, labels batch-processed through
ABBYY each OCR output file saved as individual text file tied to
barcode no. individual text files merged into Excel spreadsheet, in
which data can be searched, grouped, and parsed parsed fields
pushed to database Challenges increasing accuracy of parsing
hand-written labels (now experimenting with out-sourcing) Slide 19
Data Storage Issues Botany botanical images are valuable products
of our digitization efforts, but also challenges, due to storage
demands our concern is with long-term storage (archiving) of
uncompressed, original images have encouraged home institutions of
our partners to step up, but some unable/unwilling our solution for
now is storage on portable drives, but this is tenuous fix and not
reliable enough for truly archival storage Entomology no major
issues Slide 20 Christiane Weirauch University of California
Riverside Slide 21 Subcontract Management Setup 7 collaborating
institutions, 27 subawards Benefit: long-term data capture across
>30 institutions Issues 1) Delays: administrative and accounting
issues 2) Database selection: which one to use? 3) Training: onsite
versus remote training? 4) Tracking productivity of subawards not
using PBI database Solutions/suggestions 1) Streamlined
administrative and accounting procedures 2) Encourage use of a
default database; more discussion 3) Combination of onsite and
remote training and monitoring 4) Regular contact with subawards
Slide 22 Unique Specimen Identifiers (USIs) AMNH Matrix-code labels
Setup: Matrix codes (barcode scanner) and string of prefix and
8-digit number (human eye) encode the same unique identifier
Benefit: Tracking of specimens; connect images to records Format:
Prefix (8 characters): acronym and identifier: e.g., UCRC_ENT
XXXXXXXX Non-standard USIs: accepted in the database Exceptions:
collections that were previously databased without USIs (e.g.,
Aphidoidea, certain mirid taxa) Slide 23 Collection Staging
Organizing, sorting, and identifying specimens in preparation for
databasing Importance: highest identification level and accuracy
will yield most useful data for future applications Priority:
well-curated and well-identified collections TTD: limited budget
for staging by experts; very successful for, e.g., Miridae and
Membracidae Issue: routine staging more time-consuming than
anticipated Possible solution: budget for graduate students or post
docs to help with staging (and training/supervision of databasing
crew) Slide 24 Tri-trophic concept: Hemiptera, plants, parasitoids
Capture of host data New TTD records: 26% with host records
(compared to 24% previously databased); added >800 new hosts
Challenges of integrating parasitoid data Level of identification
of parasitoids (undescribed species; accurate identification
requires skilled personnel) Level of host identification (e.g.,
white fly) Incorporation of host information from secondary sources
(e.g., taxonomic literature)? On the right track; prioritize
specimens with quality host records & integrate secondary host
information Slide 25 Katja Seltmann The American Museum of Natural
History Slide 26 Efficiency of Data Capture: Insects Total as of
October 17, 2012 = 198,409 Includes Illinois, Texas, and Kansas All
20 subcontracts are digitizing now 53 contributors for ttd-tcn
project Numbers from NHCR database (central database at AMNH 11
subcontracts) $20,000 in equipment costs Specimens per min average:
3-3.5min/specimen (range 1.2-6) Cost per specimen: $.93 (includes
equipment) Peak in July (more hours digitizing) 65 collecting
events on Christmas Day Slide 27 Efficiency of Data Capture: Plants
All but three institutions up and running As of October 9, 2012
have 102,651 images 3 of 15 institutions not yet begun 4 plant
collections report: $30482.51 equipment costs $.73 cents a specimen
image The unmentioned curator volunteerism 4-8 hrs/week depending
on institution/taxon ~19 hours a week total Slide 28 Training
Methods: Insects (NHCR Database) Curators also training (sexing
specimens, database) Online training via Skype Digitizers clubhouse
(building community) Online manuals Online videos Remote training
Using central db can access quality of data Flag when new name is
entered Flag when more than 10 specimens entered in one min by one
person Flag when exact duplicate collecting events or localities
(check training) Slide 29 Training Methods: Plants Site visits to
subcontract institutions Kim Watson, Melissa Tulig Install imaging
equipment Personal involvement Slide 30 Quality Assessment of
Transformed Records (NHCR) Determination Completeness Note Language
(A,B,B) ; (A,A,A) ; (A,C,B) Slide 31 Present total:1487 9134 Canada
14 96 USA 1441 8564 Mexico 32 474 Georeferencing: NHCR database
130,000 specimen records Slide 32 Georeferencing: NHCR database
GEOLocate (North America) Discover Life validation Centralized and
controlled georeferencing (NYBG, AMNH) Volunteer georeferencing
Slide 33 Difficult data Issues: specimen relationships Slide 34
Difficult data Issues: means for curation? Slide 35 Summary and
Predictions: over 50,000 locality records from NHCR will reach 1
million new specimen records for insects (harder to predict for
plants at the moment) less than $1 a specimen (inclusive) Arthropod
(NHCR) data concerns will become more central as other groups come
online Slide 36 Thanks to National Science Foundation co-PIs and
collaborators http://tcn.amnh.org
